I have the same problem. As it turns out, Rhinehart recommends against installing these on the '16 Street Glide for that reason. I dropped the left side passenger peg down as far as it will go and I made a spacer out of a piece of 5/8" thick aluminum and mounted it between the peg assembly and the frame. Gave me enough clearance to flip the pegs up. I'll be replacing the exhaust next winter. I like the sound and performance but the heat off of the left side is too uncomfortable. I'm also tired of cleaning boot marks off of it after riding 2-up.
Same problem. Went with the 15 peg mount. Never really liked how the pipes installed and didn't like how the exhaust pipe ran next to left passenger foot. Changed exhaust to Rinehart slimline duals